Variant report

Variant	rs17669033
Chromosome Location	chr16:72290415-72290416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11075925	0.95[EUR][1000 genomes]
rs11646048	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12598534	0.90[EUR][1000 genomes]
rs16970769	1.00[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs16970785	0.85[EUR][1000 genomes]
rs17669057	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17669164	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4238965	0.94[EUR][1000 genomes]
rs57749102	0.89[EUR][1000 genomes]
rs62051119	0.84[ASN][1000 genomes]
rs62058275	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62058278	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62058280	0.97[EUR][1000 genomes]
rs958990	0.94[EUR][1000 genomes]
rs9635525	0.90[EUR][1000 genomes]
rs9940976	0.94[CEU][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1059599	chr16:72219769-72342170	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1066473	chr16:72229094-72373598	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv906897	chr16:72283147-72326375	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17669033	ZFHX3	cis	parietal	SCAN
rs17669033	HP	cis	multi-tissue	Pritchard
rs17669033	PHLPP2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72278600-72290600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:72289000-72291600	Enhancers	NHDF-Ad	bronchial
3	chr16:72289400-72290800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr16:72289400-72291200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr16:72289600-72290600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr16:72289600-72291000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr16:72289600-72291000	Enhancers	HMEC	breast
8	chr16:72289600-72291400	Enhancers	Osteobl	bone
9	chr16:72289800-72290800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr16:72289800-72291200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:72289800-72291400	Enhancers	NHLF	lung
12	chr16:72290000-72290800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:72290000-72291200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr16:72290000-72291200	Enhancers	Ovary	ovary
15	chr16:72290000-72291400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr16:72290000-72291400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr16:72290000-72291600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr16:72290000-72291800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr16:72290200-72291000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:72290200-72291200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr16:72290400-72291400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr16:72290400-72291400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr16:72290400-72291400	Enhancers	HepG2	liver
24	chr16:72290400-72291600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr16:72290400-72291600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr16:72290400-72316800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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